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r975: asmstat without CIGAR/NM

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This commit is contained in:
Heng Li
2020-03-22 19:16:43 -04:00
parent 6a4b9f9082
commit e2451e497a
1 changed files with 4 additions and 6 deletions
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misc/paftools.js
+4 -6
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@@ -1,6 +1,6 @@
#!/usr/bin/env k8 #!/usr/bin/env k8
var paftools_version = '2.17-r949-dirty'; var paftools_version = '2.17-r975-dirty';
/***************************** /*****************************
***** Library functions ***** ***** Library functions *****
@@ -688,11 +688,9 @@ function paf_asmstat(args)
qinfo[t[0]].bp = []; qinfo[t[0]].bp = [];
if (t.length < 9 || t[5] == "*") continue; if (t.length < 9 || t[5] == "*") continue;
if (!/\ttp:A:[PI]/.test(line)) continue; if (!/\ttp:A:[PI]/.test(line)) continue;
if ((m = /\tcg:Z:(\S+)/.exec(line)) == null) continue; var cigar = (m = /\tcg:Z:(\S+)/.exec(line)) != null? m[1] : null;
var cigar = m[1]; var NM = (m = /\tNM:i:(\d+)/.exec(line)) != null? parseInt(m[1]) : null;
if ((m = /\tNM:i:(\d+)/.exec(line)) == null) continue; var diff = cigar != null && NM != null? compute_diff(cigar, NM) : 0;
var NM = parseInt(m[1]);
var diff = compute_diff(cigar, NM);
t[2] = parseInt(t[2]); t[2] = parseInt(t[2]);
t[3] = parseInt(t[3]); t[3] = parseInt(t[3]);
t[7] = parseInt(t[7]); t[7] = parseInt(t[7]);